Reference "Sequence divergence of rice microsatellites in Oryza and other plant species"

Reference ID

7066

Title

Sequence divergence of rice microsatellites in Oryza and other plant species

Source

Mol Genet Genomics, 2002, vol. 268, pp. 331-343

Authors (3)

Chen-X	Cho-Y-G
McCouch-S-R

Abstract

To determine the basis of genetic variation at microsatellite loci, eleven
primer pairs, developed to amplify microsatellite markers in rice, were
evaluated for their ability to amplify a PCR product and for both electromorphic
and sequence-based polymorphism of the resulting products in 12 plant samples,
including representatives from six different species within the genus Oryza and
one genotype each from Zea (maize), Triticum (wheat) and Arabidopsis. PCR
amplification was reliable in the four O. sativa samples as well as in the
closely related Oryza relatives with AA genomes, while only 73% (8/11) of
primers amplified in the BB/CC and CC genomes of Oryza, and 27% (3/11) amplified
in the other genera. Three out of seven DNA fragments that were amplified from
all genera were determined to be orthologous to their rice counterparts. A total
of 115 amplicons were detected using polyacrylamide gel electrophoresis and
these clustered into 74 distinct electromorphs. Sequencing of 108 amplicons
revealed size homoplasy, exposing 13 new sequence-based variants. Allelic
diversity within a species was predominantly due to changes in the number of
repeats in the microsatellite region, but the frequency of insertions/deletions
(indels) and base substitutions increased as the genetic distance between
samples increased. This study suggests that electromorph size polymorphism is an
adequate measure of genetic difference in studies involving closely-related
individuals, but that when phylogenetic or evolutionary inferences are being
made over longer time scales, evaluation of SSR variation at the sequence level
is essential.